In .emacs

(defun hide-references-hook ()
  (save-excursion
    (let (lim)
      (goto-char (point-min))
      (re-search-forward (concat "^" (regexp-quote mail-header-separator) "$"))
      (setq lim (match-beginning 0))
      (goto-char (point-min))
      (cond ((re-search-forward "^References:.*\n\\([ \t].*\n\\)*" lim t)
	     (let ((o (make-overlay (match-beginning 0) (match-end 0))))
	       (overlay-put o 'invisible t)))))))

(defun hide-in-reply-to-hook ()
  (save-excursion
    (let (lim)
      (goto-char (point-min))
      (re-search-forward (concat "^" (regexp-quote mail-header-separator) "$"))
      (setq lim (match-beginning 0))
      (goto-char (point-min))
      (cond ((re-search-forward "^In-Reply-To:.*\n\\([ \t].*\n\\)*" lim t)
	     (let ((o (make-overlay (match-beginning 0) (match-end 0))))
	       (overlay-put o 'invisible t)))))))

(add-hook 'vm-mail-mode-hook 'hide-references-hook)
(add-hook 'vm-mail-mode-hook 'hide-in-reply-to-hook)